Abstract: Provided herein are systems and methods for the controlled surface modification of a material substrate, including, for example, generation of nanostructures, crystallographic or morphologic alterations and the removal of defects, changes in chemical composition and bond structure and the creation of thermodynamic metastable states. The provided systems and methods utilize one or more directed energetic particle beams with independently controlled parameters (e.g. incident angle, fluence, flux, energy, species, etc.) to precisely and efficiently generate enhanced surface properties beyond those of conventional plasma kinetic roughening.